(Extended Scene) of Starbuck and Helo on Caprica, in search of her apartment.

A flashback that reveals the source of Colonel Tigh's knowledge of Cylon boarding tactics.

Colonel Tigh receives a call from his wife, who is scared. Tigh tells her about the gun he has loaded in his quarters and orders her to hunker down and shoot anything that "moves without knocking first". She frightfully hunkers down in a corner of their quarters with the gun drawn.

(Extended Scene) Colonel Tigh argues with Lee Adama over Adama's powers as a prisoner and an officer.

Six warns Baltar to abandon his Raptor crew. Six also tells him that he will be the only one to see Earth.

Starbuck and Helo discuss Sharon; Commander Adama and his party track Roslin and find Elosha's grave. Roslin asks Apollo if she has made a mistake.

Commandar Adama and Roslin talk about their decisions and their costs.

(Extended Scene) Baltar tells Cottle that he thinks he might have gotten some shrapnel in his head during the crash on Kobol.

Baltar thinks he truly has gone mad, and Six tells him to enjoy his psychosis.

Billy tells Roslin that he is an atheist. Apollo apologizes to his father saying his mutiny was not based on their relationship.

Note: Although put together as a single scene on DVD, both seem to be two different scenes as they are proceeded by the same jumping-off point, suggesting that one was intended to play in place of the other. However, they don't appear to take place concurrently as evident by Tyrol's position in both scenes.

With Six at his side, still in her casual attire, Baltar comments on what might be the "deeper meaning" of the Sharon currently being held in the specially built brig were he not insane.

Kara Thrace returns to her quarters and takes out her figurines of the Lords Artemis and Aphrodite. "It's good to be home," she says.

Thrace is at Galactica's memorial wall and seems depressed that she has no one to leave a memorial for herself.

(Extended Scene) Starbuck reacts to the Tyrol/Helo fight. While Tyrol and Apollo talk about grounding the Viper, the Cylon logic bomb makes the engines start up on a Viper that Seelix was working on and Tyrol chews her out.

Cally tells Tyrol that she is not sorry she killed Boomer, that it had to be done, and Tyrol does not forgive her.

(Extended Scene) Slightly longer Adama and Dualla sparring.

Number Six reacts to Adama's dismissal of Baltar and says he'll see something truly amazing today.

(Extended Scene) When Tigh tries to talk Adama out of using Sharon, Number Six pushes Baltar to convince Adama that he can trust Sharon. As Sharon inserts the fiber-optic com link into her arm, Number Six notes that even after the way she's been treated, Sharon still wants to belong among the crew.

Tyrol and Caprica-Sharon's conversation at the end of the episode. Tyrol and Cally go back to work.

There are no deleted scenes for this episode on the official site, nor on any DVD set. This is probably because almost all of these deleted scenes were re-edited into the Director's Cut of "Pegasus" included in the R1 Season 2.5 and the R2 Season 2 DVD sets.

Dualla visits Lee Adama, who is pouring himself a drink. Dualla informs him that Pegasus wants to know about his ETA back to Pegasus. Adama tells her to notify them that he is on his way back and as corrects her on his lower rank of lieutenant. He goes on to tell her that the rank change doesn't really matter to him anymore and that he isn't sure about what does. They discuss how "frakked up things are" at present and talk about the arrival of Pegasus as well as the choices Pegasus made. Adama emotes that the reasons for them going out there and fighting and dying aren't clear to him anymore. He then leaves.

Scene 5: Apollo gives Shevon an extra 100 cubits to buy "something nice for Paya". In return, Shevon gives him a small picture holder, which was her father's. Despite his objections, he takes the picture holder, which is traded for information in a later scene aboard Prometheus. That scene was deleted as well.

Scene 9/10: Hoshi discovers the body of Commander Fisk, after the latter has been garroted by Phelan's henchman.

Scene 18: On Galactica's flight deck, Apollo exits the Raptor only to be welcomed aboard by Dualla, who is asked to direct Lee to Admiral Adama's quarters. Dualla confronts Lee regarding his avoidance of her, telling him that she overheard what he told Kara Thrace after the destruction of the Resurrection Ship and his near-death experience. He claims that he was "sick, delirious" and that "whatever [he] was feeling, [he] never meant to dump it on [her]". She calls him out on it, claiming that she thought she was the only one who sometimes believed that she was "better off on Caprica" with the dead. He then chastises her voicing this feeling, despite harboring it himself. After climbing up the ladder to the upper deck, he gets a flashback of looking down on Gianne, his former fiancé, with whom he broke up with prior to the Cylon attack.

Scene 25: Apollo reports to Pegasus's CIC. He asks to report to Commander Trammel, but Pegasus's new XO, Renner, informs him that Trammel is on his way to Galactica for "meet and greet" with Admiral Adama. When Apollo requests to see all logs, duty rosters and security reports, Renner begins his spiel about running warships for 20 years and is insulted that Pegasus crewmen are not running the investigation. Renner also laments that Pegasus was fine until "Galactica showed up" and that Adama can take his investigation and go "frak himself". Apollo then pins Renner to the table, saying that there was a time where he would have agreed with him. Renner orders the readied Marines to stand down, and Lee warns Renner that if he should "say another word against my father, [that] next time, you won't get up" and leaves the CIC.

Note: Barry Trammel would later be renamed to Barry Garner due to legal issues resulting from someone actually having that name. Also, Renner is never seen or mentioned again in the series.

Scene 39 (extended): Apollo regains consciousness in Shevon's quarters on Cloud 9 after being attack by Phelan's men. When he goes to lay down on the bed after the altercation, the scene transitions to a flashback where Shevon talks to Lee about Gianne, commenting that it's a "pretty name"; Lee reveals that it took him weeks to pronounce it correctly, although Gianne never corrected him, and that Gianne herself hated the name since no one could ever pronounce it correctly. After she comments that he must have truly loved her, he remarks that he wondered whether he really did. The flashback ends, resuming on the corpse of Fisk's killer with a bullet hole in his head and Lee calling for help.

Scene 46-46A: Apollo is on Prometheus attempting to find Phelan. When walking the corridors, he is stopped by Linden. Apollo asks Linden where Phelan is, but he doesn't reveal anything until Lee gives him something to trade. After a slight altercation, Lee trades off Shevon's pocket picture holder and gets his information which leads him to Phelan's bar. Apollo opens the hatch and is stopped by a guard, who he disables, as well as a second guard that comes charging down the corridor. As Apollo is viciously punching this second guard, a third henchman surprises him by putting a gun to his head, commenting: "Ever get the feeling that your living the same bad day again?"

Note: John Mann, who played Linden, also portrayed Galactica's CAG, Jackson Spencer, in the Miniseries.

Scene 47 (Extended scene): Apollo attempts to comfort Shevon after killing Phelan at the table. Shevon rebukes Apollo, saying that she can never be Gianne. There is a brief flashback when Lee tells Shevon that Gianne was pregnant; Apollo comments that he didn't think he was ready to be a father.

The following scenes were formerly available online.

After his first time with Shevon, Lee Adama says that he always wondered how it would be spending time with a prostitute.

When talking and drinking with Shevon, Apollo tells her about his relationship with his father. He reveals that he doubts if he can live up to him.

Paya and other kids are on a Raptor en route to an unknown destination. She looks outside the window and enjoys the view.

Scene 5: (Extended scene). Jo-Jo asks why the Cylon ace is called Scar, to which Kat replies that nuggets are "easy pickings". Clellan comments on Brent Baxton's watch, saying that BB should leave his watch to him so that he doesn't have to bid on it at the auction. Clellan saunters out of the pilots bunk, leaving the two nuggets bewildered about Clellan's comments about an "auction", to which the episode cuts...At the auction, Lee Adama is auctioning off a copy of Nymph, which Brendan Costanza wins. During this, Clellan looks at Baxton while pointing at his watch, which results in a concerned look on Braxton's face, as Braxton looks at his own watch.

Scene 8 pt.: Starbuck attempts to jump over the tables in the rec room. In this version, Karl Agathon attempts to pick up Thrace, but eventually sets her down in a corner nook of the lounge. Clark asks Adama whether it's always "like this", to which Adama replies that it is not and "it gets a little rowdy". The scene ends when Thrace begins to tear up.

Scene 21: The scripted version. Gaeta announces Roslin's arrival in CIC, to which everyone stands at attention. Once at ease, Roslin goes on to inform them that the mining ship has broken another drill bit, meaning a delay of eight more days. Tigh does not react well to this and goes on to say that it isn't easy sending kids off to a shooting gallery; Tigh advocates that they should just take the metal they have mined and cut their losses. Roslin replies that the mining team has discovered a rich vein of ore, enough to build two entire squadrons of Vipers. The good news is that Pegasus's production team has turned out its first combat ready Viper. Roslin sternly informs Tigh that he must respect this operation, for it is vital to the long term survival of the Fleet. After the discussion ends, a firefight is heard over the wireless, which results in Snake's death. Roslin then asks whether the destruction of the Resurrection Ship resulted in a change of Cylon tactics, which Adama replies that Thrace is working on it. The scene ends in Sharon's brig, where Sharon says that Scar may have died a dozen times.

Note: Snake doesn't die in the aired version and is later mentioned as a replacement pilot for Starbuck.

Scene 36 pt.: (Extended scene). Lee Adama tells Thrace that bright, shiny futures are overrated. Inebriated, Thrace asks whether Adama can picture himself with a wife, to which both hysterically laugh at the prospect. Thrace continues on this line of joking, saying that the Gods would give Adama a porch swing. Adama admits that he "thought about it once" and thought that a "stinky rugrat" (Thrace's words) would be nice.

Scene 63-64: Alternate ending. Kat is walking through the memorial hallway, where she hangs a picture of Reilly's girlfriend. Meanwhile, Thrace is praying over her Lords of Kobol figurines, promising to return for Samuel Anders.

The following scenes were formerly available online.

(Extended Scene) Because Thrace is late, Kat has started early with a briefing. When she finally arrives, Thrace berates Kat for starting and continues by recapitulating the Fleet's strategic situation.

Starbuck and Helo work out in the gym. The two talk about Kat's attitude, and Helo compares her to behavior to Starbuck's.

Scene 1-2: The scripted version of the flashback pertaining to Ray Abinell's death. Here, Abinell is on the phone to his wife, telling her that he is finishing up work on replacing heat sensors on Greenleaf. He then looks out the window and sees dozens of Cylon Raiders. Hurriedly, he says his goodbye to Sesha and hangs up, running down the corridor as a raider begins its strafing run. The windows of the compartment he is in are compromised and Abinell, despite his vain effort to hold on to piping that runs along the corridor, is sucked out into space.

The following scene was formerly available online.

Lee Adama and Dualla talk about their upcoming shore leave and Billy Keikeya. She says that she hasn't talked to Keikeya yet, but that she appreciates what she had with him.

Scene 9: (Extended scene). This scene starts off with Garner berating Kara Thrace for not keeping track of her pilots' whereabouts or situation. In this scene, Louis Hoshi is relieved of his post, and replaced with Abel Thornton, after failing to inform Garner that a Raptor was requesting launch clearance. Garner goes on to state that there is no excuse for the lack of cohesion that is apparent in the Pegasus crew.

Scene 35: Thrace and Lee Adama argue over giving Garner respect; Thrace believes that the people should have a leader worthy of their respect. The scene ends when a call for flight deck personnel to report to their stations is made.

Scenes 62-68: Alternate scene. The scenes that did not make the final cut for "The Captain's Hand" are the ones pertaining to Rya Kibby's attempted suicide after her abortion. Laura Roslin is looking out a window on Colonial One. Meanwhile, an orderly on Galactica discovers that Rya Kibby has overdosed on pills and lays on the sickbay bed, unconscious and with a rosary in her hand. The orderly presses what appears to be an alarm button on the panel above the bed. In a scene that made the final cut, we jump back to Colonial One, where Tory Foster brings in Sarah Porter, the Gemenese delegate to the Quorum of Twelve. Porter begins attacking Roslin over not prosecuting Kibby for going through with the abortion. Roslin replies that the grant for asylum came before the law was signed and thus no laws have been broken; Roslin also adds that Porter has her "pound of flesh" and suggests that "you take your victory and move on". Back in Galactica's sickbay, Doctor Cottle and nurses attempt to resuscitate Kibby and ultimately succeed in doing so.

Scene 69 pt.: Lee Adama jokingly asks Kara Thrace whether she has a brain. As they hug, Dualla walks in; Thrace excuses herself and states that she'll put the boots outside for them. Dualla then states that "you're not going to tell me about promotions, are you?" and discuss Adama's promotion to commander of Pegasus and how their relationship will work now that they are separated from one another physically; they begin to make out after Dualla asks whether or not Thrace was joking about the boots outside the door.

The following scenes were formerly available online.

Over dinner Adama and Tigh discuss Commander Garner. Tigh wonders how he managed to lose two Raptors and complains about the general state of the ship. Adama says that he sent Apollo over to keep an eye on Garner and to give him someone he can trust. Tigh asks if Adama still thinks about making Apollo Pegasus's XO.

Note: This clears up Apollo's somewhat unclear status in the aired episode. He is not officially Garner's XO.

Tory Foster tells Roslin that they'll lose the election if they lose the Gemenese and urges her to reconsider her stance on abortion in order to win. Roslin asks her if that is also the right thing to do. Foster replies that she is not there to be Roslin's counsel or conscience, but to help her to win.

Scene 34-36: Baltar visits Gina Inviere on Cloud 9 in an attempt to convince her to orchestrate Hera's theft. Gina resists as she views Caprica Sharon as a deserter and her "half-breed child" to be no better. She also scoffs Baltar's attempts to convince her on religious grounds; Baltar's Six appears and reiterates her view that Gina is a "broken machine" who has lost her faith in God. Gina bluntly reminds Baltar that Roslin is leading him by 3 points in the current polls, which is what his energies should be focused upon. Baltar fine tunes his argument, ultimately convincing Gina that the theft of a Cylon child from Galactica would be politically destructive as it would undermine Roslin's credibility as a wartime leader.

Scene 34-36 (continued):D'Anna Biers, Tory Foster and Roslin hold a meeeting on Colonial One, where Biers attempts to convince Roslin to grant her exclusive access to Hera as word of the birth has apparently spread throughout the Fleet. After the discussion, Roslin agrees, as it would be beneficial for both parties: people can see the Cylon child as looking the same as a normal human child and Biers gets exclusive pictures.

Scene 48: Biers and Gina are on Cloud 9 discussing how they will take the child. In her camera case, Biers has built a life-support system to secret the child off Galactica, which is hidden in the bulky case. When Biers claims that "little Hera will be comfortable" in the contraption, Gina retorts that the child should not be named after a human god. When briefly discussing what they should call her, Gina says "just call her 13", which Biers favorably responds to.

Scene 54: Biers is outside of sickbay with a Marine and Layne Ishay. Ishay tells her that Biers can't see the baby. As Biers attempts to gain access, noting that Roslin herself approved the visit, Helo calls Biers a "stupid frakking vulture" when telling her that Hera is dead. Ishay claims that the baby died 20 minutes ago, which shocks Biers.

Scene 63D: Galen Tyrol is walking on the upper level of the maintenance deck. There are flashes of his dream of falling from this upper level. Over it all, Cavil is consoling the Chief, telling him that his fear is that he fears he is a Cylon, like Sharon and he should die.

Scene 78: Commander Lee Adama is laying in his bunk on Pegasus. Dualla is also present getting dressed after their sexual encounter; she comments that Adama hasn't signed the papers and she is a courier on official business. Dualla asks him whether or not he believes Roslin will lose to Baltar, Adama replies that while he doesn't know, she is a fighter and tells Dualla that Roslin may be on the wrong side of the colonization issue. He also voices his concern that Kara Thrace has yet to return from her SAR mission to Caprica.

Scene 121: Tyrol talks to Cally about Cavil, who has been revealed as another humanoid Cylon, over the deck gang's homemade liquor. He remarks that Cavil almost got him to believe that he was a Cylon and that the two Cavils were thrown out of an airlock the night before. Cally tries to drink the liquor, but can't handle it, to which they both giggle. Cally then slowly approaches Tyrol and kisses him, much to his surprise, to which Cally replies "What, you didn't know?"

Scene 123B: Baltar is on a Raptor where he has flashbacks of meeting Gina Inviere on Pegasus and their subsequent encounters on Cloud 9. This Raptor is headed to Cloud 9, where Baltar enters the ship through a hatch where two Marines are waiting and one follows to close the hatch. He is saluted by a fourth Marine as he enters a more decorative part of Cloud 9.

Scene 141 (Extended Scene): Baltar is sitting on Colonial One. Admiral Adama gives the newly elected president a report on Cloud 9's destruction and his belief that they need to strengthen internal security. Baltar rebukes him and instead states that their first priority is to the people, and to see that they are safely established on New Caprica. Once that is done, he believes that the tragedy would be put behind them. Adama bluntly retorts that Baltar is not listening; he replies that "I don't have to listen. I'm the president." Baltar orders that "Settlement begins and begins now". During their whole conversation Baltar has flashbacks to his time with Gina, which are missing from the aired version.

Tigh: Second. I was a petty officer, gunner's mate. There were 20 of us alive. We were the last line of defense guarding the magazines. It was hand to hand at the end. Man against machine. And I was just a kid. Virgin. Teenager. I'd never seen a dead person before. First one was Duncan Raverti. Deckhand Dunc. I found him in the corridor. His ribs were split open like a pig. His guts were strewn around him on the floor. You know, at first...at first I couldn't figure out why the Cylons would bother doing something like that.

Adama: Spread fear. Panic.

Tigh: No. You had to look into that red eye slit. They hated us. They hated us so much, it wasn't enough to just kill us. You know that Centurions have a stink? It's like machine oil. To this day, I get a whiff if grease or oil...I almost lose my lunch.

Adama: I was on the Galactica. We were boarded the last week of the war. By the end of the war they learned a lot. Gotten smart. Clever. They didn't head to CIC, or the magazines. Two teams. One went to secondary damage control, and the other to aux fire control. See? That's clever. Not to CIC...auxiliary. And not to primary DC, to secondary. [...] Smart. Clever. Almost 2000 guys bought the farm, that day.

Adama: Dee...eh...I can't even begin to tell you how frakked up things are right now.

Dualla: You mean ever since the Pegasus arrived.

Adama: Yeah...no...no, I don't know. I guess I thought it was them. But now, I'm not so sure we're that different. Just a step away from the choices that they made.

Dualla: Seems like a pretty important step. I don't see us raping our prisoners.

Adama: No, we haven't done that. Not yet.

Dualla: Are you saying...

Adama: Look, I don't know what I'm saying. How is that for clarity? All I know is that...well, the reason we keep going out and fighting and dying, it's just not that clear to me anymore.

The extended version of Apollo's and Starbuck's drunken chat in "Scar":

Thrace: Can you actually picture you...you actually...yourself...picture you...with a wife? (both laugh) ...with a wife and a kid and a porch swing, 'cause the Gods know you would have a little porch swing.

Adama: You know, I thought about it once.

Thrace: (laughs) You're kidding.

Adama: Yeah.

Thrace: You wanted some little stinky rugrat?

Adama: I thought it might be nice. Teach the little kid to swim, play pyramid.

Thrace: Bob and weave. Duck and cover. Frak, Lee, you should be a politician.

Adama: Garner's wrong about this, and I know that. That really isn't the point. The point is, that you owed him your respect. You owed him your loyalty. You owed him the chance to make it as commander of this ship.

Thrace: I owed him? What about what he owes us? What about having a leader who is worthy of the people he leads? Do we not deserve that?

Adama: (sighs)

Thrace: You hate it when she argues rationally, don't you? So much easier when she's foulmouthed hothead, howling at the moon, eh?